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- PDB-3uec: Crystal structure of human Survivin bound to histone H3 phosphory... -

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Basic information

Entry
Database: PDB / ID: 3uec
TitleCrystal structure of human Survivin bound to histone H3 phosphorylated on threonine-3.
Components
  • Baculoviral IAP repeat-containing protein 5
  • N-TERMINAL FRAGMENT OF HISTONE H3
KeywordsCELL CYCLE / zinc finger / phosphorylated threonine / BIR DOMAIN / CHROMOSOMAL PASSENGER COMPLEX / CELL DIVISION / MITOSIS
Function / homology
Function and homology information


survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of exit from mitosis / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / interphase microtubule organizing center / protein-containing complex localization ...survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of exit from mitosis / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / interphase microtubule organizing center / protein-containing complex localization / chromosome passenger complex / cobalt ion binding / cysteine-type endopeptidase inhibitor activity / nuclear chromosome / mitotic spindle assembly checkpoint signaling / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / SUMOylation of DNA replication proteins / mitotic cytokinesis / chromosome, centromeric region / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / centriole / positive regulation of mitotic cell cycle / tubulin binding / RHO GTPases Activate Formins / spindle microtubule / sensory perception of sound / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / kinetochore / spindle / small GTPase binding / Separation of Sister Chromatids / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / mitotic cell cycle / Neddylation / midbody / protein-folding chaperone binding / microtubule binding / Interleukin-4 and Interleukin-13 signaling / microtubule / protein heterodimerization activity / cell division / protein phosphorylation / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Baculoviral IAP repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.18 Å
AuthorsNiedzialkowska, E. / Porebski, P.J. / Cooper, D.R. / Chruszcz, M. / Wang, F. / Higgins, J.M. / Stukenberg, P.T. / Minor, W.
CitationJournal: Mol.Biol.Cell / Year: 2012
Title: Molecular basis for phosphospecific recognition of histone H3 tails by Survivin paralogues at inner centromeres.
Authors: Niedzialkowska, E. / Wang, F. / Porebski, P.J. / Minor, W. / Higgins, J.M. / Stukenberg, P.T.
History
DepositionOct 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 5
B: N-TERMINAL FRAGMENT OF HISTONE H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1709
Polymers17,3832
Non-polymers7877
Water95553
1
A: Baculoviral IAP repeat-containing protein 5
B: N-TERMINAL FRAGMENT OF HISTONE H3
hetero molecules

A: Baculoviral IAP repeat-containing protein 5
B: N-TERMINAL FRAGMENT OF HISTONE H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,34018
Polymers34,7654
Non-polymers1,57414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area4730 Å2
ΔGint-6 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.254, 70.225, 88.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-167-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Baculoviral IAP repeat-containing protein 5 / Apoptosis inhibitor 4 / Apoptosis inhibitor survivin


Mass: 16826.127 Da / Num. of mol.: 1 / Mutation: E129K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: API4, BIRC5, IAP4 / Plasmid: p8HIS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3)-RIL / References: UniProt: O15392
#2: Protein/peptide N-TERMINAL FRAGMENT OF HISTONE H3


Mass: 556.550 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 7 types, 60 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsE129K REPRESENTS A NATURAL VARIANT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% peg 8000; O.1 M MOPS 7.5; 0.1 M Magnesium acetate tetrahydrate , VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2010 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. all: 11616 / Num. obs: 11616 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 44.3 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.2
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 2.3 / Num. unique all: 586 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
REFMAC5.6.0117refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.18→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.957 / SU B: 9.5 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.159
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21488 554 4.8 %RANDOM
Rwork0.19838 ---
all0.19919 11061 --
obs0.19919 11061 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.691 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.18→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 0 40 53 1231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221199
X-RAY DIFFRACTIONr_bond_other_d0.010.02878
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.981600
X-RAY DIFFRACTIONr_angle_other_deg1.9983.0022125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3145140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22324.38657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6515204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.769157
X-RAY DIFFRACTIONr_chiral_restr0.0980.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211295
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02237
LS refinement shellResolution: 2.18→2.237 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 37 -
Rwork0.258 723 -
obs--97.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.6970.7332-1.00874.20590.41842.6869-0.12710.167-0.75060.00290.1662-0.37410.19620.038-0.0390.17490.02220.00490.1188-0.08760.1319-17.797-13.837-15.042
20.0731-0.6443-0.96586.10939.57915.4563-0.0012-0.0127-0.0205-0.01130.10320.03360.06830.1603-0.1020.2201-0.05540.02420.2261-0.08780.0958-31.777-17.962-21.306
323.06411.039310.66028.5981-5.743646.66430.20050.0623-0.0639-0.7566-0.0554-0.11870.49850.9705-0.14511.1696-0.16980.19720.1501-0.01280.0396-29.8-33.562-55.362
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 90
2X-RAY DIFFRACTION2A91 - 133
3X-RAY DIFFRACTION3A134 - 142

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